Settings: Output files: "MCSpleen16b/tmp/segment_juncs.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: MCSpleen16b/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 5098599 Using parameters --bmax 3823950 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3823950 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.5493e+06 (target: 3823949) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 1630030 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1630031 Getting block 2 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 2533341 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2533342 Getting block 3 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 2273870 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2273871 Getting block 4 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 3194581 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3194582 Getting block 5 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 1935037 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1935038 Getting block 6 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 3473733 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3473734 Getting block 7 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 3642750 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3642751 Getting block 8 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 1711047 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1711048 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4878721 fchr[G]: 10313467 fchr[T]: 15301380 fchr[$]: 20394396 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37567421 bytes to primary EBWT file: MCSpleen16b/tmp/segment_juncs.1.bt2 Wrote 5098604 bytes to secondary EBWT file: MCSpleen16b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20394396 bwtLen: 20394397 sz: 5098599 bwtSz: 5098600 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1274650 offsSz: 5098600 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 106221 numLines: 106221 ebwtTotLen: 6798144 ebwtTotSz: 6798144 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:21 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 5098599 Using parameters --bmax 3823950 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3823950 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:01 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.5493e+06 (target: 3823949) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 3044964 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3044965 Getting block 2 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 2241675 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2241676 Getting block 3 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 1854575 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1854576 Getting block 4 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 2688688 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2688689 Getting block 5 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 1598718 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1598719 Getting block 6 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:01 Sorting block of length 3730045 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3730046 Getting block 7 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 2802893 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2802894 Getting block 8 of 8 Reserving size (3823950) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 2432831 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2432832 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4878721 fchr[G]: 10313467 fchr[T]: 15301380 fchr[$]: 20394396 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37567421 bytes to primary EBWT file: MCSpleen16b/tmp/segment_juncs.rev.1.bt2 Wrote 5098604 bytes to secondary EBWT file: MCSpleen16b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20394396 bwtLen: 20394397 sz: 5098599 bwtSz: 5098600 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1274650 offsSz: 5098600 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 106221 numLines: 106221 ebwtTotLen: 6798144 ebwtTotSz: 6798144 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:18